Mercurial > repos > greg > ideas_genome_tracks
changeset 72:623f81b08310 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 21 Dec 2017 10:35:49 -0500 |
| parents | c04084f77b33 |
| children | cc517e44244e |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Wed Dec 20 13:25:36 2017 -0500 +++ b/ideas_genome_tracks.R Thu Dec 21 10:35:49 2017 -0500 @@ -103,6 +103,12 @@ chrom_len_file, tracks_dir, hub_name, short_label, long_label, state_indexes, state_colors) { # Create a trackDb.txt file that includes each state. para_files <- list.files(path=input_dir_para, full.names=TRUE); + ###### + # The following is temporary and will be eliminated when there + # are multiple .para files. See the comments in the for loop + # below. + data_frame <- read.table(para_files[1], comment="!", header=T); + ###### base_track_file_name <- paste(tracks_dir, hub_name, sep=""); cells = create_track(input_dir_state, chrom_len_file, base_track_file_name); if (!is.null(state_indexes)) { @@ -125,7 +131,9 @@ for (i in 1:length(cells)) { # Get the color for the current state. if (is.null(state_indexes) || !is.element(i, s_indexes)) { - data_frame <- read.table(para_files[i], comment="!", header=T); + ###### + # This is for future use since there is currently only a single .para file. + # data_frame <- read.table(para_files[i], comment="!", header=T); color_hex_code <- create_heatmap(data_frame); } else { # Use the selected color for the current state. @@ -194,3 +202,4 @@ # Create the primary HTML dataset. create_primary_html(opt$output_trackhub, tracks_dir, opt$build); +